ok, just tested several things and found probably the triggering event for the change.
Here is how to reproduce it:
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create new project
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add landscape
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add new object collision channel (object type) any name
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set object type of the landscape to the new one (change to custom collision)
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add nav mesh bounds volume
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set agent height to (any than 144)
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save project
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close project
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open project
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change the object type of the landscape
RESULT: the agent height will change back to 144
Funny thing is that sometimes it resets by it self when you open the project.